Bestwrench,
The prevailing opinions seem to be that most of the spots are polishing artifacts. While some of them may well be, I'll stay with my suggestion that there are several varieties of carbides visible. The nominal chemistry you mentioned is typical of tool steels. Ignoring the water spots and pits for a moment. The vague lines comprised of small black spots still look like grain boundary precipitated chromium carbides to me. The larger spots could be tungsten carbides. If these are in fact pits(and I can't say for certain that they aren't) then they're either gas porosity(in spite of the vacuum degas) or tear-out from the polishing process.
I agree with deadrange's comments about the possibility of MnS inclusions. Given the nominal chemistry this is not possible.
My eyes didn't pick up the grey surrounding some of the spots that others have stated is indicative of a calcium treated steel. I'll defer to them in this, as it's not something I'm familiar with...
Is there a specific reason for not etching this specimen? are you preserving the as-polished surface for micro-hardness testing? Or some other test?
Etching this steel would also serve to help clear up some of this mystery....
Deadrange's suggestion to play with the depth of focus and see what appears makes sense to me as well. If your optical microscope has enough magnification, you might be able to resolve more details about any pits in the surface.
If the university you're working with has an SEM, then the pits could be examined in more detail. Gas porosity would have a very smooth, spherical interior. A rough for faceted interior surface on the pits would indicate something torn out or dissolved during the polishing(although this seems unlikely to me)...
David Benson
Benson's Mobile Welding & Fabrication